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Population Structure of Coimbatore Canes Developed in a Century of Sugarcane Breeding in India

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Abstract

One hundred years have passed since the inception of sugarcane breeding in India and the country witnessed 9.58-fold increase in sugarcane production. A major factor for this success was due to the impact of Coimbatore canes (Co canes) developed at ICAR-Sugarcane Breeding Institute, Coimbatore, India, which dominate the sugarcane area in the country. This study was conducted to gain knowledge about population structure of the improved genetic material comprising 1453 Co canes for their judicious utilization in sugarcane improvement activities. Field trials were conducted by pooling these Co canes developed during 1918 to 2017 for sugar yield and its component traits. Population structure develops due to non- random mating of individuals resulting in varying allelic frequency among different sub-populations. Population structure analysis divided the Co canes into four sub-populations (subpopulation). The strength and weakness of each sub-population for important yield and juice quality traits revealed from the study are summarized. Accordingly, the Co canes in subpopulations 3 and 4 appeared promising for breeding for varietal development, and combination of Co canes belonging to two different groups with high expression of specific traits could be used as parents for trait specific genetic enhancement. These subpopulations were in turn classified into many sub-subpopulations among which sub-subpopulation 4 of subpopulation1 and sub-subpopulation 3 of subpopulation 3 were the unique populations identified for number of millable canes (NMC) and Hand Refractometer brix (HRB) at 240 days, respectively, whereas for other traits there were more number of superior subpopulations. The result of the study is expected to aid parental selection to harness the best out of the genetic diversity available in the commercial gene pool to achieve faster genetic gain and to improve precision of sugarcane breeding.

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Availability of Data and Material

The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

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References

  • Ahmed, A.O., and A. Obeid. 2010. Genetic divergence among sugarcane genotypes (Saccharum spp.) for cane yield attributes and Quality determinants. African Journal of Agricultural Research 5 (16): 2103–2107.

    Google Scholar 

  • Ali, A., Y.B. Pan, Q.N. Wang, J.D. Wang, J.L. Chen, and S.J. Gao. 2019. Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers. Scientific Reports 9: 395. https://doi.org/10.1038/s41598-018-36630-7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amalraj, V.A., and N. Balasundaram. 2018. Status of Sugarcane Genetic Resources in India. Bureau De Rédaction 148: 26–31.

    Google Scholar 

  • Banerjee, N., A. Siraree, S. Yadav, S. Kumar, J. Singh, S. Kumar, D.K. Pandey, and R.K. Singh. 2015. Marker-trait associations for sucrose and yield contributing traits in sugarcane (Saccharum spp Hybrid). Euphytica 205: 185–201.

    Article  CAS  Google Scholar 

  • Bisht, R., A.S. Jeena, D. Koujalagi, S.P. Singh, and K.A. Khan. 2017. Estimation of genetic diversity among sugarcane (Saccharum species complex) clones. Journal of Applied and Natural Science 9 (3): 1469–1474. https://doi.org/10.31018/jans.v9i3.1386.

    Article  Google Scholar 

  • Earl, D.A., and B.M. VonHoldt. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4 (2): 359–361.

    Article  Google Scholar 

  • Edme, S.J., J.D. Miller, B. Glaz, P.Y.P. Tai, and J.C. Comstock. 2005. Genetic contribution to yield gains in the Florida sugar industry across 33 years. Crop Science 45 (1): 92–97.

    Google Scholar 

  • Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14 (8): 2611–2620.

    Article  CAS  Google Scholar 

  • Federer, W.T. 1956. Augmented designs Hawaiian Planters’. Record 55: 191–208.

    Google Scholar 

  • Hammer, O., D.A.T. Harper, and P.D. Ryan. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4 (1): 9.

    Google Scholar 

  • Hemaprabha, G., Alarmelu, S., and R.M. Shanthi. 2012. Relative Performance of Co canes developed at Sugarcane Breeding Institute for sucrose content Proc Intern Symposium on New Paradigms in sugarcane research held at Coimbatore from October 15–18 p: 103–105

  • Hemaprabha, G., Alarmelu, S., and R.M. Shanthi. 2015. Genetic improvement of Co canes over decades Proceedings of XI Joint Convention of The Sugar Technologists association of India and the Deccan Sugar technologists association (India) 4 -6 September 2015 Goa p: 219–227

  • Hemaprabha G., S. Alarmelu, R.M. Shanthi, and B. Ram B. 2017a. Database of Coimbatore canes. (1918–2017) ICAR-Sugarcane breeding institute, Coimbatore. ISBN: 978–93–85267–08–6.

  • Hemaprabha, G., K. Mohanraj, S. Alarmelu, and B. Ram. 2017b. Relative performance of Coimbatore canes (Co canes) for major component traits of yield and quality and an analysis of their genealogies to measure genetic gain over a century of sugarcane breeding at ICAR Sugarcane Breeding Institute. In: International Symposium on Sugarcane Research Since Co 205: 100 Years and Beyond (SucroSym 2017) held from 18–21 Sep 2018 at Coimbatore, p 98–102.

  • Hurtado, P.L., Y. Ruiz, C. Santos, C. Phillips, A. Carracedo, and M. Lareu. 2013. An overview of STRUCTURE: applications parameter settings and supporting software. Frontiers in Genetics 4: 98.

    Google Scholar 

  • Jeswiet, J. 1925. Bijdrage tot de systematiek van het geslacht Saccharum Mededeelingen Proefstation. Java-Suikerindustrie. 12: 391–404.

    Google Scholar 

  • Kuwahara, K., R. Suzuki, Y. Itoa, T. Mikami, and Y. Onodera. 2014. An analysis of genetic differentiation and geographical variation of spinach germplasm using SSR markers. Plant Genetic Resources 12: 185–190.

    Article  Google Scholar 

  • Li, Y., R. Guan, Z. Liu, Y. Ma, L. Wang, L. Li, F. Lin, W. Luan, P. Chen, Z. Yan, Y. Guan, L. Zhu, X. Ning, M.J.M. Sumlders, W. Li, R. Piao, Y. Cui, Z. Yu, M. Guan, R. Chang, A. Hou, A. Shi, B. Zhang, S. Zhu, and L. Qiu. 2008. Genetic structure and diversity of cultivated soybean (Glycine max (L) Merr) landraces in China. TAG. Theoretical and Applied Genetics. 117: 857–871 (PMID: 18587557).

    Article  CAS  Google Scholar 

  • Manechini, J.R.V., J.B. da Costa, B.T. Pereira, L.A. Carlini-Garcia, M.A. Xavier, M.G.A. Landell, and L.A. Pinto. 2018. Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers. PLoS ONE 13 (4): e0195623.

    Article  Google Scholar 

  • Nayak, S.N., J. Song, A. Villa, B. Pathak, T.A. Silva, X. Yang, J. Todd, N.C. Glynn, D.N. Kuhn, B. Glaz, R.A. Gilbert, J.C. Comstock, and J. Wang. 2014. Promoting utilization of Saccharum spp genetic resources through genetic diversity analysis and core collection construction. PLoS ONE 9: e110856.

    Article  Google Scholar 

  • Padmanabhan, T.S.S., and G. Hemaprabha. 2018. Genetic diversity and population structure among 133 elite genotypes of sugarcane (Saccharum spp) for use as parents in sugarcane varietal improvement. 3 Biotech 8 (8): 339.

    Article  Google Scholar 

  • Pathy, T.L., and K. Mohanraj. 2021. Estimating best linear unbiased predictions (BLUP) for yield and quality traits in sugarcane. Sugar Tech. https://doi.org/10.1007/s12355-021-01011-4.

    Article  Google Scholar 

  • R Core Team. 2019. R: A language and environment for statistical computing R Foundation for Statistical Computing. Vienna, Austria. URL https://www.R-projectorg/

  • Ram, B., G. Hemaprabha, B.D. Singh, et al. 2021. History and current status of sugarcane breeding, germplasm development and molecular biology in India. Sugar Tech. https://doi.org/10.1007/s12355-021-01015-0.

    Article  Google Scholar 

  • Sharma, M.D., U. Dobhal, P. Singh, S. Kumar, A. Gaur, S.P. Singh, A.S. Jeena, E.P. Koshy, and S. Kumar. 2014. Assessment of genetic diversity among sugarcane cultivars using novel microsatellite markers. African Journal of Biotechology 13: 1444–1451.

    Article  Google Scholar 

  • Singh, R.K., S.N. Jena, S. Khan, S. Yadav, N. Banarjee, S. Raghuvanshi, B. Vasudha, S.K. Dattamajumder, R. Kapur, S. Solomon, M. Swapna, S. Srivastava, and A.K. Tyagi. 2013. Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene 524: 309–329.

    Article  CAS  Google Scholar 

  • Singh, R.K., N. Banerjee, M.S. Khan, S. Yadav, S. Kumar, S.K. Duttamajumder, R.J. Lal, J.D. Patel, H. Guo, D. Zhang, and A.H. Paterson. 2016. Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping. Molecular Genetics and Genomics 291: 1363–1377.

    Article  CAS  Google Scholar 

  • Widyasari, W.B., L.K. Putra, M.R.R. Ranomahera, et al. 2021. Historical notes, germplasm development, and molecular approaches to support sugarcane breeding program in Indonesia. Sugar Tech. https://doi.org/10.1007/s12355-021-01069-0.

    Article  Google Scholar 

  • Zhang, X., H. Zhang, L. Li, H. Lan, Z. Ren, D. Liu, L. Wu, J. Jaqueth, B. Li, G. Pan, and S. Gao. 2016. Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers. BMC Genomics 17: 697. https://doi.org/10.1186/s12864-016-3041-3.

    Article  PubMed  PubMed Central  Google Scholar 

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Authors

Contributions

Hemaprabha: Conceptualization, Methodology, Writing- Original draft preparation, Lakshmi Pathy: Formal analysis, draft preparation and Editing, Mohanraj: Formal analysis, Reviewing, Alarmelu: Investigation, Resources, Bakshi Ram: Visualization, Supervision.

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Correspondence to G Hemaprabha.

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G, H., Pathy, T.L., Mohanraj, K. et al. Population Structure of Coimbatore Canes Developed in a Century of Sugarcane Breeding in India. Sugar Tech 24, 1449–1460 (2022). https://doi.org/10.1007/s12355-021-01093-0

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